Multiple virus and viroid detection and strain separation via multiplex reverse transcription-polymerase chain reaction

Vegetatively propagated plants free from virus- or viroid-induced diseases are integral of the success of many agricultural and horticultural sectors. Reverse transcription - polymerase chain reaction (RT-PCR) has emerged as an effective method to detect the presence of causal agents and has been used as a management strategy to ensure virus- or viroid-free propagation. Advances in understanding virus and viroid genome structures and the availability of genomic sequences of viruses and viroids (and their strains) have made it possible to create primers for specific RTPCR. This has permitted RT-PCR to evolve into a technique that can simultaneously detect multiple pathogens in a single sample. Multiplex RT-PCR can reduce cost and save time. A further modification of multipex RT-PCR, termed competitive RT-PCR, with a single-antisense and multiple-sense primers, has been developed. It facilitates simultaneous identification and differentiation of a group of virus strains. The methodology of multiplex RT-PCR and its modified (competitive) RT-PCR version for potato virus and viroid detection and strain differentiation are reviewed here.